The consumption of “ready-to-eat” agricultural products is recently increasing and the safety of these agricultural products is forefront of public concerns. The 120 samples of paprikas, strawberries and tomatoes, which are the representative exported agricultural products, were purchased at the department stores and discount stores in Daejeon. And we determined the microbiological and parasitological contamination level of these agricultural products using culture media, multiplex PCR, commercial bacterial detection kit and microscopy, and also evaluated the decontamination method. Mean counts of total aerobic bacteria from these agricultural products ranged from 1.3×104 CFU/g to 1.8×105 CFU/g, and mean counts of coliforms ranged from 1.4×103 CFU/g to 9.6×103 CFU/g. There was no significant difference in the level of bacterial contamination between the agricultural products from department stores and the ones from discount stores. Strawberry showed the highest contamination level for the bacteria and we also found the unidentified parasite eggs. Enterobacter cloacae was the most frequently isolated bacteria strain, but no food poisoning pathogenic bacteria except Staphylococcus aureus was isolated from the products by multiplex PCR. Compared to unwashed products, tab water-washed ones showed 80% decrease of the counts of total aerobic bacteria on the agricultural products, and the rates decreased more by incorporating detergent or ultrasonic wave treatment. We concluded that the biological contamination levels among paprikas, strawberries and tomatoes were the highest in strawberries, but there were not significant difference according to distribution systems.